Starting phenix.real_space_refine on Wed Sep 17 11:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zen_60040/09_2025/8zen_60040.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 12 5.49 5 S 48 5.16 5 C 5244 2.51 5 N 1439 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8388 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1162 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2993 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 369} Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2993 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 369} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2207 SG CYS C 244 45.271 50.394 53.953 1.00 65.54 S ATOM 2668 SG CYS C 305 42.868 51.887 51.962 1.00 70.70 S ATOM 5200 SG CYS D 244 33.584 56.661 82.900 1.00 86.54 S ATOM 5661 SG CYS D 305 34.077 56.824 86.308 1.00 71.41 S Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8388 At special positions: 0 Unit cell: (70.192, 103.576, 136.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 12 15.00 O 1643 8.00 N 1439 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 323.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 305 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 244 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 191 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 244 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 305 " 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 47.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 69 through 84 removed outlier: 4.120A pdb=" N GLN B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 116 through 120 removed outlier: 4.117A pdb=" N GLN B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.503A pdb=" N MET B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.742A pdb=" N LYS B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 removed outlier: 3.909A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 192 through 211 Processing helix chain 'C' and resid 122 through 142 removed outlier: 3.802A pdb=" N LYS C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.517A pdb=" N TYR C 146 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.692A pdb=" N ILE C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.730A pdb=" N ARG C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.881A pdb=" N ASN C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.984A pdb=" N LEU C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 428 through 444 Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.794A pdb=" N SER C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 477 Processing helix chain 'C' and resid 486 through 490 Processing helix chain 'D' and resid 121 through 142 removed outlier: 3.569A pdb=" N GLU D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 150 removed outlier: 4.012A pdb=" N LYS D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.550A pdb=" N ILE D 180 " --> pdb=" O GLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.103A pdb=" N LEU D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.685A pdb=" N LEU D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.569A pdb=" N SER D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 388 " --> pdb=" O ALA D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.727A pdb=" N MET D 491 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 removed outlier: 3.721A pdb=" N GLN E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.538A pdb=" N CYS E 101 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.686A pdb=" N ASN E 108 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.533A pdb=" N GLN E 119 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.525A pdb=" N GLN E 131 " --> pdb=" O MET E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.530A pdb=" N PHE E 136 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 177 through 191 Processing helix chain 'E' and resid 192 through 211 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.744A pdb=" N VAL E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.615A pdb=" N VAL C 155 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA C 153 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER C 332 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE C 235 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 334 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 237 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL C 336 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 239 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.740A pdb=" N MET C 392 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'C' and resid 278 through 279 Processing sheet with id=AA5, first strand: chain 'C' and resid 410 through 415 removed outlier: 3.608A pdb=" N ASP C 415 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N GLY D 370 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 332 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 235 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 334 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 237 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL D 336 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 239 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 392 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N GLY D 370 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER D 332 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE D 235 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 334 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 237 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL D 336 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 239 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 220 through 222 Processing sheet with id=AA9, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AB1, first strand: chain 'D' and resid 411 through 414 Processing sheet with id=AB2, first strand: chain 'D' and resid 446 through 447 removed outlier: 6.581A pdb=" N SER D 446 " --> pdb=" O ASN E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 374 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2468 1.33 - 1.46: 1369 1.46 - 1.58: 4596 1.58 - 1.70: 9 1.70 - 1.82: 76 Bond restraints: 8518 Sorted by residual: bond pdb=" O16 IHP C 501 " pdb=" P6 IHP C 501 " ideal model delta sigma weight residual 1.672 1.565 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O12 IHP D 501 " pdb=" P2 IHP D 501 " ideal model delta sigma weight residual 1.675 1.568 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O14 IHP C 501 " pdb=" P4 IHP C 501 " ideal model delta sigma weight residual 1.671 1.575 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O15 IHP D 501 " pdb=" P5 IHP D 501 " ideal model delta sigma weight residual 1.675 1.589 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O12 IHP C 501 " pdb=" P2 IHP C 501 " ideal model delta sigma weight residual 1.675 1.591 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 8513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 11389 3.45 - 6.89: 104 6.89 - 10.34: 21 10.34 - 13.79: 5 13.79 - 17.24: 3 Bond angle restraints: 11522 Sorted by residual: angle pdb=" CB MET E 158 " pdb=" CG MET E 158 " pdb=" SD MET E 158 " ideal model delta sigma weight residual 112.70 129.94 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C1 IHP D 501 " pdb=" C2 IHP D 501 " pdb=" C3 IHP D 501 " ideal model delta sigma weight residual 108.51 123.79 -15.28 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C2 IHP D 501 " pdb=" O12 IHP D 501 " pdb=" P2 IHP D 501 " ideal model delta sigma weight residual 123.98 108.89 15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C4 IHP D 501 " pdb=" C5 IHP D 501 " pdb=" C6 IHP D 501 " ideal model delta sigma weight residual 109.60 121.71 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C1 IHP D 501 " pdb=" C6 IHP D 501 " pdb=" C5 IHP D 501 " ideal model delta sigma weight residual 108.26 119.67 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 11517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 5045 32.46 - 64.92: 208 64.92 - 97.38: 27 97.38 - 129.83: 8 129.83 - 162.29: 2 Dihedral angle restraints: 5290 sinusoidal: 2185 harmonic: 3105 Sorted by residual: dihedral pdb=" CA MET C 296 " pdb=" C MET C 296 " pdb=" N GLY C 297 " pdb=" CA GLY C 297 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C6 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C2 IHP C 501 " pdb=" O12 IHP C 501 " ideal model delta sinusoidal sigma weight residual 61.05 -136.66 -162.29 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C4 IHP C 501 " pdb=" C2 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " ideal model delta sinusoidal sigma weight residual 60.90 -137.89 -161.21 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 1317 0.957 - 1.913: 0 1.913 - 2.870: 0 2.870 - 3.826: 0 3.826 - 4.783: 8 Chirality restraints: 1325 Sorted by residual: chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.52 2.26 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" C5 IHP C 501 " pdb=" C4 IHP C 501 " pdb=" C6 IHP C 501 " pdb=" O15 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.42 2.34 -4.76 2.00e-01 2.50e+01 5.66e+02 chirality pdb=" C2 IHP D 501 " pdb=" C1 IHP D 501 " pdb=" C3 IHP D 501 " pdb=" O12 IHP D 501 " both_signs ideal model delta sigma weight residual False -2.52 2.10 -4.62 2.00e-01 2.50e+01 5.34e+02 ... (remaining 1322 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 121 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR D 121 " 0.042 2.00e-02 2.50e+03 pdb=" O THR D 121 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 122 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 158 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C MET E 158 " -0.039 2.00e-02 2.50e+03 pdb=" O MET E 158 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 159 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 163 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ILE E 163 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE E 163 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL E 164 " -0.010 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 557 2.73 - 3.27: 9120 3.27 - 3.81: 14087 3.81 - 4.36: 17260 4.36 - 4.90: 29083 Nonbonded interactions: 70107 Sorted by model distance: nonbonded pdb=" OE1 GLU D 368 " pdb=" OG SER E 106 " model vdw 2.187 3.040 nonbonded pdb=" N GLN E 152 " pdb=" OE1 GLN E 152 " model vdw 2.209 3.120 nonbonded pdb=" OG SER D 304 " pdb=" OD2 ASP D 307 " model vdw 2.221 3.040 nonbonded pdb=" O GLN E 119 " pdb=" NE2 GLN E 121 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP D 189 " pdb=" NZ LYS D 270 " model vdw 2.253 3.120 ... (remaining 70102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 217)) selection = (chain 'E' and resid 67 through 217) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.870 8528 Z= 1.508 Angle : 0.917 17.237 11522 Z= 0.449 Chirality : 0.361 4.783 1325 Planarity : 0.004 0.035 1473 Dihedral : 18.554 162.292 3272 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.76 % Allowed : 26.67 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1061 helix: 0.57 (0.26), residues: 393 sheet: 0.93 (0.45), residues: 122 loop : -0.12 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 386 TYR 0.029 0.001 TYR D 350 PHE 0.024 0.002 PHE D 124 TRP 0.007 0.001 TRP D 482 HIS 0.007 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 8518) covalent geometry : angle 0.91748 (11522) hydrogen bonds : bond 0.19390 ( 359) hydrogen bonds : angle 6.67705 ( 1020) metal coordination : bond 0.26258 ( 6) Misc. bond : bond 0.67215 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.349 Fit side-chains REVERT: B 135 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7260 (ptmm) REVERT: B 168 LYS cc_start: 0.7747 (tppt) cc_final: 0.6843 (tptt) REVERT: B 209 LYS cc_start: 0.8128 (tppp) cc_final: 0.7544 (ttpt) REVERT: B 210 GLU cc_start: 0.6755 (tp30) cc_final: 0.6449 (tp30) REVERT: C 141 ASN cc_start: 0.7892 (m-40) cc_final: 0.7639 (m-40) REVERT: C 273 LYS cc_start: 0.7203 (tmtt) cc_final: 0.6868 (ptpt) REVERT: C 299 ARG cc_start: 0.6420 (mmm-85) cc_final: 0.6188 (mmm160) REVERT: C 346 ARG cc_start: 0.7377 (ttp80) cc_final: 0.7033 (ttp-110) REVERT: D 221 THR cc_start: 0.8058 (t) cc_final: 0.7662 (p) REVERT: D 222 LYS cc_start: 0.7956 (tttp) cc_final: 0.7683 (tptp) REVERT: D 273 LYS cc_start: 0.7234 (tppt) cc_final: 0.6409 (tmtt) REVERT: D 406 THR cc_start: 0.8585 (m) cc_final: 0.8286 (p) REVERT: D 491 MET cc_start: 0.7746 (mtp) cc_final: 0.7493 (mtm) REVERT: E 142 LYS cc_start: 0.6835 (pmtt) cc_final: 0.6426 (mppt) REVERT: E 152 GLN cc_start: 0.6617 (mp10) cc_final: 0.3839 (tm-30) REVERT: E 198 LYS cc_start: 0.7652 (mmpt) cc_final: 0.7157 (mtmt) REVERT: E 209 LYS cc_start: 0.7401 (tmmt) cc_final: 0.6835 (ttmm) outliers start: 16 outliers final: 7 residues processed: 176 average time/residue: 0.6473 time to fit residues: 120.2557 Evaluate side-chains 120 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 186 ASN C 461 GLN C 476 GLN E 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133454 restraints weight = 9633.856| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.95 r_work: 0.3402 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8528 Z= 0.136 Angle : 0.733 12.051 11522 Z= 0.350 Chirality : 0.051 0.648 1325 Planarity : 0.004 0.034 1473 Dihedral : 7.655 59.106 1233 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.28 % Allowed : 24.26 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.26), residues: 1061 helix: 0.78 (0.25), residues: 407 sheet: 1.40 (0.51), residues: 95 loop : -0.20 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 190 TYR 0.012 0.001 TYR D 205 PHE 0.017 0.002 PHE D 124 TRP 0.006 0.001 TRP D 473 HIS 0.008 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8518) covalent geometry : angle 0.73282 (11522) hydrogen bonds : bond 0.04284 ( 359) hydrogen bonds : angle 4.85691 ( 1020) metal coordination : bond 0.00858 ( 6) Misc. bond : bond 0.00177 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 168 LYS cc_start: 0.7958 (tppt) cc_final: 0.7149 (tptt) REVERT: B 198 LYS cc_start: 0.8275 (mttt) cc_final: 0.7868 (mtmt) REVERT: B 201 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6715 (mt0) REVERT: B 209 LYS cc_start: 0.8167 (tppp) cc_final: 0.7345 (pttt) REVERT: C 136 TYR cc_start: 0.8010 (m-80) cc_final: 0.7738 (m-80) REVERT: C 284 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6572 (pt0) REVERT: C 299 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6736 (mmm160) REVERT: C 346 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7197 (ttp-110) REVERT: C 347 LYS cc_start: 0.8247 (tppt) cc_final: 0.7934 (mptt) REVERT: C 371 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: C 462 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7987 (mp0) REVERT: D 263 ASN cc_start: 0.5812 (OUTLIER) cc_final: 0.5555 (t0) REVERT: D 338 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6311 (mt-10) REVERT: D 471 ILE cc_start: 0.8097 (mm) cc_final: 0.7828 (mm) REVERT: E 122 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 142 LYS cc_start: 0.6776 (pmtt) cc_final: 0.6460 (mppt) REVERT: E 152 GLN cc_start: 0.6814 (mp10) cc_final: 0.3986 (tm-30) REVERT: E 198 LYS cc_start: 0.7728 (mmpt) cc_final: 0.7349 (mtmt) REVERT: E 201 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: E 209 LYS cc_start: 0.7596 (tmmt) cc_final: 0.7042 (ttmm) outliers start: 39 outliers final: 12 residues processed: 145 average time/residue: 0.6104 time to fit residues: 93.8573 Evaluate side-chains 125 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 ASN E 131 GLN E 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131961 restraints weight = 9623.015| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.74 r_work: 0.3388 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8528 Z= 0.133 Angle : 0.647 11.642 11522 Z= 0.322 Chirality : 0.047 0.389 1325 Planarity : 0.004 0.038 1473 Dihedral : 7.591 53.668 1227 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.83 % Allowed : 22.83 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1061 helix: 0.78 (0.25), residues: 409 sheet: 1.85 (0.53), residues: 87 loop : -0.16 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 190 TYR 0.012 0.001 TYR D 205 PHE 0.014 0.002 PHE D 124 TRP 0.007 0.001 TRP D 473 HIS 0.009 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8518) covalent geometry : angle 0.64692 (11522) hydrogen bonds : bond 0.03559 ( 359) hydrogen bonds : angle 4.53551 ( 1020) metal coordination : bond 0.00241 ( 6) Misc. bond : bond 0.00049 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 76 GLN cc_start: 0.7734 (mt0) cc_final: 0.7413 (mp10) REVERT: B 112 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6491 (t0) REVERT: B 168 LYS cc_start: 0.8085 (tppt) cc_final: 0.7206 (tptt) REVERT: B 198 LYS cc_start: 0.8167 (mttt) cc_final: 0.7735 (mtmt) REVERT: B 201 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: B 209 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7439 (pttt) REVERT: C 150 LYS cc_start: 0.7680 (mmtp) cc_final: 0.7136 (mmpt) REVERT: C 266 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7655 (mtp85) REVERT: C 284 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6597 (pt0) REVERT: C 299 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6988 (mmm160) REVERT: C 346 ARG cc_start: 0.7298 (ttp80) cc_final: 0.7078 (ttm-80) REVERT: C 347 LYS cc_start: 0.8260 (tppt) cc_final: 0.7973 (mptt) REVERT: C 368 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: C 493 THR cc_start: 0.9232 (t) cc_final: 0.8947 (m) REVERT: D 176 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6981 (mtp85) REVERT: D 263 ASN cc_start: 0.5854 (OUTLIER) cc_final: 0.5640 (t0) REVERT: D 405 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7622 (ttm170) REVERT: D 471 ILE cc_start: 0.8171 (mm) cc_final: 0.7891 (mm) REVERT: E 122 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: E 127 MET cc_start: 0.8229 (tmt) cc_final: 0.7930 (tmm) REVERT: E 142 LYS cc_start: 0.6750 (pmtt) cc_final: 0.6405 (mppt) REVERT: E 157 GLN cc_start: 0.5516 (OUTLIER) cc_final: 0.5258 (tt0) REVERT: E 198 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7406 (mtpt) REVERT: E 201 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: E 209 LYS cc_start: 0.7590 (tmmt) cc_final: 0.7124 (ttmm) outliers start: 44 outliers final: 12 residues processed: 145 average time/residue: 0.6430 time to fit residues: 98.6739 Evaluate side-chains 124 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 157 GLN Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN B 201 GLN C 379 GLN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124004 restraints weight = 9875.243| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.74 r_work: 0.3291 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8528 Z= 0.255 Angle : 0.744 13.696 11522 Z= 0.363 Chirality : 0.055 0.713 1325 Planarity : 0.004 0.035 1473 Dihedral : 7.936 56.693 1227 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.15 % Allowed : 21.41 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1061 helix: 0.39 (0.25), residues: 406 sheet: 1.61 (0.49), residues: 102 loop : -0.36 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 248 TYR 0.018 0.002 TYR C 453 PHE 0.017 0.002 PHE E 136 TRP 0.011 0.002 TRP D 482 HIS 0.013 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 8518) covalent geometry : angle 0.74431 (11522) hydrogen bonds : bond 0.04282 ( 359) hydrogen bonds : angle 4.84953 ( 1020) metal coordination : bond 0.00545 ( 6) Misc. bond : bond 0.00069 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6620 (t0) REVERT: B 135 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7803 (mtmm) REVERT: B 168 LYS cc_start: 0.8291 (tppt) cc_final: 0.7308 (tptt) REVERT: B 177 PHE cc_start: 0.7848 (m-80) cc_final: 0.7646 (m-80) REVERT: B 198 LYS cc_start: 0.8322 (mttt) cc_final: 0.7965 (mppt) REVERT: B 209 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7679 (ttpt) REVERT: C 150 LYS cc_start: 0.7778 (mmtp) cc_final: 0.7165 (mmpt) REVERT: C 266 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7849 (mtp85) REVERT: C 284 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: C 299 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7140 (mtp180) REVERT: C 346 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7162 (ttm-80) REVERT: C 347 LYS cc_start: 0.8400 (tppt) cc_final: 0.8079 (mptt) REVERT: C 371 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: C 375 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: C 405 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7276 (ttm110) REVERT: C 410 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: C 493 THR cc_start: 0.9314 (t) cc_final: 0.9113 (m) REVERT: D 176 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6910 (mtp85) REVERT: D 263 ASN cc_start: 0.6007 (OUTLIER) cc_final: 0.5660 (t0) REVERT: D 275 MET cc_start: 0.8337 (ptp) cc_final: 0.8122 (ptp) REVERT: D 346 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6671 (mmm160) REVERT: D 405 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7983 (ttm-80) REVERT: D 494 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6936 (pp) REVERT: E 78 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6512 (mt) REVERT: E 122 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: E 137 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7281 (mtmm) REVERT: E 142 LYS cc_start: 0.6813 (pmtt) cc_final: 0.6472 (mppt) REVERT: E 198 LYS cc_start: 0.7824 (mmpt) cc_final: 0.7486 (mtpt) REVERT: E 201 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: E 209 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7153 (ttmm) outliers start: 56 outliers final: 24 residues processed: 154 average time/residue: 0.5888 time to fit residues: 96.2708 Evaluate side-chains 142 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129640 restraints weight = 9676.115| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.71 r_work: 0.3355 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8528 Z= 0.117 Angle : 0.592 9.177 11522 Z= 0.299 Chirality : 0.045 0.373 1325 Planarity : 0.003 0.039 1473 Dihedral : 7.809 57.694 1227 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.50 % Allowed : 24.26 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1061 helix: 0.65 (0.25), residues: 414 sheet: 1.52 (0.53), residues: 94 loop : -0.25 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 475 TYR 0.009 0.001 TYR D 205 PHE 0.011 0.001 PHE D 124 TRP 0.005 0.001 TRP D 482 HIS 0.012 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8518) covalent geometry : angle 0.59217 (11522) hydrogen bonds : bond 0.03397 ( 359) hydrogen bonds : angle 4.45767 ( 1020) metal coordination : bond 0.00089 ( 6) Misc. bond : bond 0.00024 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.311 Fit side-chains REVERT: B 76 GLN cc_start: 0.7822 (mt0) cc_final: 0.7584 (mp10) REVERT: B 112 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6631 (t0) REVERT: B 135 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7810 (mtmm) REVERT: B 168 LYS cc_start: 0.8269 (tppt) cc_final: 0.7243 (tptt) REVERT: B 177 PHE cc_start: 0.7789 (m-80) cc_final: 0.7571 (m-80) REVERT: B 209 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7640 (ttpt) REVERT: B 210 GLU cc_start: 0.6951 (tp30) cc_final: 0.6691 (tp30) REVERT: C 150 LYS cc_start: 0.7595 (mmtp) cc_final: 0.7245 (mmtt) REVERT: C 266 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7813 (mtp-110) REVERT: C 284 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: C 299 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7277 (mmp-170) REVERT: C 347 LYS cc_start: 0.8361 (tppt) cc_final: 0.8068 (mptt) REVERT: C 368 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: C 410 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7298 (mmt) REVERT: C 493 THR cc_start: 0.9303 (t) cc_final: 0.9070 (m) REVERT: D 176 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7004 (mtp85) REVERT: D 263 ASN cc_start: 0.5906 (OUTLIER) cc_final: 0.5618 (t0) REVERT: D 405 ARG cc_start: 0.8321 (ttm170) cc_final: 0.8047 (ttm170) REVERT: D 494 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6949 (pp) REVERT: E 122 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: E 137 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7228 (mtmm) REVERT: E 198 LYS cc_start: 0.7809 (mmpt) cc_final: 0.7511 (mtpt) REVERT: E 201 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: E 209 LYS cc_start: 0.7747 (tmmt) cc_final: 0.7190 (ttmm) outliers start: 41 outliers final: 17 residues processed: 149 average time/residue: 0.6215 time to fit residues: 98.0400 Evaluate side-chains 140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 201 GLN C 341 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.172467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125497 restraints weight = 9666.242| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.71 r_work: 0.3304 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8528 Z= 0.186 Angle : 0.637 11.304 11522 Z= 0.320 Chirality : 0.048 0.456 1325 Planarity : 0.004 0.036 1473 Dihedral : 7.268 56.813 1226 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.38 % Allowed : 23.93 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1061 helix: 0.55 (0.25), residues: 413 sheet: 1.44 (0.49), residues: 104 loop : -0.32 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 248 TYR 0.011 0.001 TYR C 453 PHE 0.018 0.002 PHE E 136 TRP 0.009 0.001 TRP D 482 HIS 0.013 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8518) covalent geometry : angle 0.63705 (11522) hydrogen bonds : bond 0.03708 ( 359) hydrogen bonds : angle 4.56079 ( 1020) metal coordination : bond 0.00346 ( 6) Misc. bond : bond 0.00052 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.347 Fit side-chains REVERT: B 76 GLN cc_start: 0.7949 (mt0) cc_final: 0.7691 (mp10) REVERT: B 112 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.6686 (t0) REVERT: B 135 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7837 (mtmm) REVERT: B 168 LYS cc_start: 0.8365 (tppt) cc_final: 0.7306 (tptt) REVERT: B 209 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7558 (ttpt) REVERT: C 150 LYS cc_start: 0.7662 (mmtp) cc_final: 0.7202 (mmtt) REVERT: C 266 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7825 (mtp85) REVERT: C 284 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: C 299 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7247 (mmm160) REVERT: C 347 LYS cc_start: 0.8435 (tppt) cc_final: 0.8119 (mptt) REVERT: C 371 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6804 (pm20) REVERT: C 405 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7263 (ttm110) REVERT: C 410 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7296 (mmt) REVERT: C 493 THR cc_start: 0.9305 (t) cc_final: 0.9068 (m) REVERT: D 263 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.5640 (t0) REVERT: D 371 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6235 (mm-30) REVERT: D 405 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7932 (ttm-80) REVERT: D 494 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7228 (pp) REVERT: E 78 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6452 (mt) REVERT: E 122 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: E 137 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7375 (mtmm) REVERT: E 174 SER cc_start: 0.5114 (p) cc_final: 0.4846 (m) REVERT: E 198 LYS cc_start: 0.7849 (mmpt) cc_final: 0.7515 (mtpt) REVERT: E 201 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: E 209 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7228 (ttmm) outliers start: 49 outliers final: 23 residues processed: 151 average time/residue: 0.6552 time to fit residues: 104.5973 Evaluate side-chains 146 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 494 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128008 restraints weight = 9744.935| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.67 r_work: 0.3350 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.121 Angle : 0.595 8.514 11522 Z= 0.300 Chirality : 0.045 0.331 1325 Planarity : 0.003 0.038 1473 Dihedral : 7.008 59.491 1226 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.83 % Allowed : 24.15 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1061 helix: 0.72 (0.25), residues: 413 sheet: 1.44 (0.50), residues: 104 loop : -0.25 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 176 TYR 0.008 0.001 TYR D 205 PHE 0.024 0.001 PHE B 177 TRP 0.006 0.001 TRP D 482 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8518) covalent geometry : angle 0.59465 (11522) hydrogen bonds : bond 0.03313 ( 359) hydrogen bonds : angle 4.39681 ( 1020) metal coordination : bond 0.00163 ( 6) Misc. bond : bond 0.00026 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6650 (t0) REVERT: B 135 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7807 (mtmm) REVERT: B 168 LYS cc_start: 0.8252 (tppt) cc_final: 0.7216 (tptt) REVERT: B 198 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7840 (mppt) REVERT: C 150 LYS cc_start: 0.7610 (mmtp) cc_final: 0.6908 (mmpt) REVERT: C 266 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7816 (mtp85) REVERT: C 284 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6347 (pt0) REVERT: C 299 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7285 (mmp-170) REVERT: C 347 LYS cc_start: 0.8396 (tppt) cc_final: 0.8112 (mptt) REVERT: C 368 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: C 375 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6739 (pp20) REVERT: C 410 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7268 (mmt) REVERT: C 493 THR cc_start: 0.9296 (t) cc_final: 0.9039 (m) REVERT: D 263 ASN cc_start: 0.5821 (OUTLIER) cc_final: 0.5579 (t0) REVERT: D 371 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.6043 (mm-30) REVERT: E 78 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6327 (mt) REVERT: E 122 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: E 137 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7429 (mtmm) REVERT: E 174 SER cc_start: 0.5119 (p) cc_final: 0.4837 (m) REVERT: E 198 LYS cc_start: 0.7845 (mmpt) cc_final: 0.7583 (mtpt) REVERT: E 201 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: E 206 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6571 (m) REVERT: E 209 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7244 (ttmm) outliers start: 44 outliers final: 22 residues processed: 146 average time/residue: 0.6168 time to fit residues: 95.5490 Evaluate side-chains 145 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128172 restraints weight = 9706.700| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.66 r_work: 0.3349 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.126 Angle : 0.601 8.367 11522 Z= 0.303 Chirality : 0.045 0.334 1325 Planarity : 0.004 0.037 1473 Dihedral : 6.911 59.613 1226 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.17 % Allowed : 25.03 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1061 helix: 0.79 (0.25), residues: 413 sheet: 1.63 (0.54), residues: 94 loop : -0.23 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 475 TYR 0.008 0.001 TYR D 205 PHE 0.020 0.001 PHE B 177 TRP 0.006 0.001 TRP D 482 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8518) covalent geometry : angle 0.60125 (11522) hydrogen bonds : bond 0.03259 ( 359) hydrogen bonds : angle 4.35108 ( 1020) metal coordination : bond 0.00178 ( 6) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.6690 (t0) REVERT: B 135 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7791 (mtmm) REVERT: B 168 LYS cc_start: 0.8282 (tppt) cc_final: 0.7224 (tptt) REVERT: B 198 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7790 (mppt) REVERT: B 209 LYS cc_start: 0.8161 (tppp) cc_final: 0.7574 (ttpt) REVERT: B 210 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6402 (mm-30) REVERT: C 150 LYS cc_start: 0.7561 (mmtp) cc_final: 0.6845 (mmpt) REVERT: C 266 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7831 (mtp85) REVERT: C 284 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6302 (pt0) REVERT: C 299 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7309 (mmp-170) REVERT: C 347 LYS cc_start: 0.8403 (tppt) cc_final: 0.8101 (mptt) REVERT: C 368 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 410 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7253 (mmt) REVERT: C 493 THR cc_start: 0.9295 (t) cc_final: 0.9028 (m) REVERT: D 263 ASN cc_start: 0.5833 (OUTLIER) cc_final: 0.5554 (t0) REVERT: E 78 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6345 (mt) REVERT: E 122 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: E 137 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7403 (mtmm) REVERT: E 146 LYS cc_start: 0.7499 (tmtm) cc_final: 0.7261 (tptp) REVERT: E 174 SER cc_start: 0.5125 (p) cc_final: 0.4849 (m) REVERT: E 191 CYS cc_start: 0.6957 (m) cc_final: 0.6655 (m) REVERT: E 198 LYS cc_start: 0.7824 (mmpt) cc_final: 0.7572 (mtpt) REVERT: E 201 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: E 206 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6558 (m) REVERT: E 209 LYS cc_start: 0.7733 (tmmt) cc_final: 0.7253 (ttmm) outliers start: 38 outliers final: 22 residues processed: 143 average time/residue: 0.6283 time to fit residues: 95.3983 Evaluate side-chains 141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 45 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 overall best weight: 0.2690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130812 restraints weight = 9738.495| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.66 r_work: 0.3380 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8528 Z= 0.109 Angle : 0.587 8.063 11522 Z= 0.298 Chirality : 0.044 0.276 1325 Planarity : 0.003 0.038 1473 Dihedral : 6.771 59.856 1226 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.29 % Allowed : 26.34 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1061 helix: 0.91 (0.25), residues: 414 sheet: 1.43 (0.53), residues: 96 loop : -0.16 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 344 TYR 0.008 0.001 TYR D 205 PHE 0.024 0.001 PHE B 177 TRP 0.005 0.001 TRP D 482 HIS 0.003 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8518) covalent geometry : angle 0.58725 (11522) hydrogen bonds : bond 0.03097 ( 359) hydrogen bonds : angle 4.24798 ( 1020) metal coordination : bond 0.00076 ( 6) Misc. bond : bond 0.00020 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6704 (t0) REVERT: B 168 LYS cc_start: 0.8315 (tppt) cc_final: 0.7190 (tptt) REVERT: B 198 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7806 (mppt) REVERT: B 209 LYS cc_start: 0.8144 (tppp) cc_final: 0.7544 (ttpt) REVERT: C 150 LYS cc_start: 0.7501 (mmtp) cc_final: 0.6732 (mmpt) REVERT: C 266 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7822 (mtp85) REVERT: C 284 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6374 (pt0) REVERT: C 299 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: C 347 LYS cc_start: 0.8394 (tppt) cc_final: 0.8097 (mptt) REVERT: C 368 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 410 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7218 (mmt) REVERT: C 493 THR cc_start: 0.9273 (t) cc_final: 0.9003 (m) REVERT: D 263 ASN cc_start: 0.5789 (OUTLIER) cc_final: 0.5543 (t0) REVERT: E 137 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7477 (mtmm) REVERT: E 174 SER cc_start: 0.5090 (p) cc_final: 0.4859 (m) REVERT: E 191 CYS cc_start: 0.6921 (m) cc_final: 0.6478 (m) REVERT: E 198 LYS cc_start: 0.7810 (mmpt) cc_final: 0.7559 (mtpt) REVERT: E 201 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: E 206 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6511 (m) REVERT: E 209 LYS cc_start: 0.7606 (tmmt) cc_final: 0.7215 (ttmm) outliers start: 30 outliers final: 17 residues processed: 138 average time/residue: 0.6209 time to fit residues: 91.0797 Evaluate side-chains 130 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.175527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129574 restraints weight = 9663.571| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.65 r_work: 0.3367 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.129 Angle : 0.609 7.944 11522 Z= 0.307 Chirality : 0.045 0.329 1325 Planarity : 0.004 0.036 1473 Dihedral : 6.733 59.786 1225 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.18 % Allowed : 25.80 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1061 helix: 0.91 (0.25), residues: 414 sheet: 1.40 (0.53), residues: 96 loop : -0.19 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 128 TYR 0.008 0.001 TYR D 205 PHE 0.023 0.001 PHE B 177 TRP 0.006 0.001 TRP D 482 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8518) covalent geometry : angle 0.60857 (11522) hydrogen bonds : bond 0.03216 ( 359) hydrogen bonds : angle 4.30491 ( 1020) metal coordination : bond 0.00201 ( 6) Misc. bond : bond 0.00028 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 112 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6680 (t0) REVERT: B 168 LYS cc_start: 0.8405 (tppt) cc_final: 0.7296 (tptt) REVERT: B 198 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7818 (mppt) REVERT: B 209 LYS cc_start: 0.8175 (tppp) cc_final: 0.7552 (ttpt) REVERT: C 150 LYS cc_start: 0.7507 (mmtp) cc_final: 0.6765 (mmpt) REVERT: C 266 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7837 (mtp85) REVERT: C 284 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6454 (pt0) REVERT: C 299 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7342 (mtp180) REVERT: C 347 LYS cc_start: 0.8404 (tppt) cc_final: 0.8108 (mptt) REVERT: C 368 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: C 410 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7257 (mmt) REVERT: C 493 THR cc_start: 0.9288 (t) cc_final: 0.9004 (m) REVERT: D 149 GLU cc_start: 0.7138 (pt0) cc_final: 0.6786 (pm20) REVERT: D 263 ASN cc_start: 0.5776 (OUTLIER) cc_final: 0.5549 (t0) REVERT: D 405 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.8005 (ttp-110) REVERT: E 137 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7462 (mtmm) REVERT: E 161 LYS cc_start: 0.7372 (mmmm) cc_final: 0.7166 (mmmm) REVERT: E 174 SER cc_start: 0.5266 (p) cc_final: 0.5065 (m) REVERT: E 191 CYS cc_start: 0.6923 (m) cc_final: 0.6612 (m) REVERT: E 198 LYS cc_start: 0.7811 (mmpt) cc_final: 0.7558 (mtpt) REVERT: E 201 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: E 206 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6593 (m) REVERT: E 209 LYS cc_start: 0.7638 (tmmt) cc_final: 0.7197 (ttmm) outliers start: 29 outliers final: 19 residues processed: 132 average time/residue: 0.6244 time to fit residues: 87.4050 Evaluate side-chains 131 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.173154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127721 restraints weight = 9638.019| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.63 r_work: 0.3344 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8528 Z= 0.152 Angle : 0.639 9.536 11522 Z= 0.320 Chirality : 0.046 0.383 1325 Planarity : 0.004 0.037 1473 Dihedral : 6.784 59.565 1225 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.84 % Allowed : 26.02 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1061 helix: 0.83 (0.25), residues: 414 sheet: 1.39 (0.53), residues: 96 loop : -0.20 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.007 0.001 TYR D 205 PHE 0.022 0.002 PHE B 177 TRP 0.006 0.001 TRP D 482 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8518) covalent geometry : angle 0.63871 (11522) hydrogen bonds : bond 0.03384 ( 359) hydrogen bonds : angle 4.38063 ( 1020) metal coordination : bond 0.00277 ( 6) Misc. bond : bond 0.00039 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.17 seconds wall clock time: 50 minutes 27.24 seconds (3027.24 seconds total)